Inter- and intramolecular fluorescence quenching of organic dyes by tryptophan

Bioconjug Chem. Nov-Dec 2003;14(6):1133-9. doi: 10.1021/bc0341324.


Steady-state and time-resolved fluorescence measurements were performed to elucidate the fluorescence quenching of oxazine, rhodamine, carbocyanine, and bora-diaza-indacene dyes by amino acids. Among the natural amino acids, tryptophan exhibits the most pronounced quenching efficiency. Especially, the red-absorbing dyes ATTO 655, ATTO 680, and the oxazine derivative MR 121 are strongly quenched almost exclusively by tryptophan due to the formation of weak or nonfluorescent ground-state complexes with association constants, K(ass.), ranging from 96 to 206 M(-1). Rhodamine, fluorescein, and bora-diaza-indacene derivatives that absorb at shorter wavelengths are also quenched substantially by tyrosine residues. The quenching of carbocyanine dyes, such as Cy5, and Alexa 647 by amino acids can be almost neglected. While quenching of ATTO 655, ATTO 680, and the oxazine derivative MR121 by tryptophan is dominated by static quenching, dynamic quenching is more efficient for the two bora-diaza-indacene dyes Bodipy-FL and Bodipy630/650. Labeling of the dyes to tryptophan, tryptophan-containing peptides, and proteins (streptavidin) demonstrates that knowledge of these fluorescence quenching processes is crucial for the development of fluorescence-based diagnostic assays. Changes in the fluorescence quantum yield of dye-labeled peptides and proteins might be used advantageously for the quantification of proteases and specific binding partners.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry
  • Boron Compounds / chemistry
  • Carbocyanines / chemistry
  • Fluorescent Dyes / chemistry*
  • Molecular Structure
  • Oxazines / chemistry
  • Peptides / chemistry
  • Proteins / chemistry
  • Rhodamines / chemistry
  • Spectrometry, Fluorescence
  • Tryptophan / chemistry*


  • Amino Acids
  • Boron Compounds
  • Carbocyanines
  • Fluorescent Dyes
  • Oxazines
  • Peptides
  • Proteins
  • Rhodamines
  • Tryptophan